Update changes to reflect only the change in order of steps. Fix output files.

CHANGELOG.md

@@ -9,7 +9,7 @@
 * Make pull references from BioHPC default (including in biohpc.config)
 * Start using new gudmaprbk dockerhub (images autobuilt)
 * Moved consistency checks to be fully python
-* Added back parallel form of trim_galore and now use fastqc after trim step
+* Changed order of steps so that fastqc is done after the trim step
 
 *Known Bugs*
 * Datahub reference pull uses dev.gudmap.org as source until referencencs are placed on production

workflow/rna-seq.nf

@@ -341,7 +341,7 @@ process trimData {
 
   output:
     path ("*.fq.gz") into fastqsTrim
-    path ("*.fastq.gz") into fastqs_fastqc
+    path ("*.fastq.gz") includeInput:true into fastqs_fastqc
     path ("*_trimming_report.txt") into trimQC
     path ("readLength.csv") into inferMetadata_readLength
 
@@ -881,7 +881,7 @@ process alignData {
 }
 
 // Replicate rawBam for multiple process inputs
-rawBam.set {
+rawBam.into {
   rawBam_dedupData
 }